Nextflow workflow report

[confident_bose] (resumed run)

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 102.

The full error message was:

Error executing process > 'STAR_Fusion (34)'

Caused by:
  Process `STAR_Fusion (34)` terminated with an error exit status (102)

Command executed:

  set -eou pipefail
  
  STAR --genomeDir $PWD/ctat_genome_lib_build_dir/ref_genome.fa.star.idx 			--runThreadN 8 			--readFilesIn TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r1.fq.gz TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r2.fq.gz 			--outFileNamePrefix TARGET.20.3812482.03A.01R_ 			--outReadsUnmapped None 			--twopassMode Basic 			--twopass1readsN -1 			--readFilesCommand "gunzip -c" 			--outSAMunmapped Within 			--outSAMtype BAM SortedByCoordinate 			--limitBAMsortRAM 63004036730 			--outSAMattributes NH HI NM MD AS nM jM jI XS 			--chimSegmentMin 12 			--chimJunctionOverhangMin 12 			--chimOutJunctionFormat 1 			--alignSJDBoverhangMin 10 			--alignMatesGapMax 100000 			--alignIntronMax 100000 			--alignSJstitchMismatchNmax 5 -1 5 5 			--outSAMattrRGline ID:GRPundef 			--chimMultimapScoreRange 3 			--chimScoreJunctionNonGTAG -4 		  --chimMultimapNmax 20 			--chimNonchimScoreDropMin 10 			--peOverlapNbasesMin 12 			--peOverlapMMp 0.1 			--chimFilter banGenomicN
  
  
  /usr/local/src/STAR-Fusion/STAR-Fusion --genome_lib_dir $PWD/ctat_genome_lib_build_dir 	  	--chimeric_junction "TARGET.20.3812482.03A.01R_Chimeric.out.junction" 			--left_fq TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r1.fq.gz 			--right_fq TARGET-20-3812482-03A-01R_RBS_withJunctionsOnGenome_dupsFlagged_r2.fq.gz 	  	--CPU 8 	  	--FusionInspector inspect 	  	--examine_coding_effect 	  	--denovo_reconstruct 	  	--output_dir TARGET.20.3812482.03A.01R_
  
  
  echo ----------------------------------------
  echo "list all output files in /home/jlsmith3/scripts/STAR-fusion-NF"
  ls -1 $PWD
  
  echo -----------------------------------------
  echo "list all output files in sample directory"
  ls -1 TARGET.20.3812482.03A.01R_

Command exit status:
  102

Command output:
  Aug 26 02:43:11 ..... started STAR run
  Aug 26 02:43:11 ..... loading genome
  Aug 26 02:43:34 ..... started 1st pass mapping
  Aug 26 03:03:52 ..... finished 1st pass mapping
  Aug 26 03:03:53 ..... inserting junctions into the genome indices
  Aug 26 03:07:46 ..... started mapping
  Aug 26 03:46:37 ..... finished mapping
  Aug 26 03:46:40 ..... started sorting BAM

Command error:
  
  EXITING because of fatal ERROR: not enough memory for BAM sorting: 
  SOLUTION: re-run STAR with at least --limitBAMsortRAM 70729026558
  Aug 26 03:46:40 ...... FATAL ERROR, exiting

Work dir:
  s3://fh-pi-meshinchi-s-nextflow-scratch/a8/2cb99ebf9a49b7c3bf22359ae0ff5a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Run times
25-Aug-2021 16:24:09 - 26-Aug-2021 02:16:05 (duration: 9h 51m 56s)
  90 succeeded  
  850 cached  
  0 ignored  
  27 failed  
Nextflow command
nextflow run -c /home/jlsmith3/nextflow.config main.nf --sample_sheet sample_sheets/TARGET_AML_Remission_JMML_APL_MDAnderson_sample_sheet.txt --star_genome_lib 's3://fh-pi-meshinchi-s-eco-public/Reference_Data/GRCh37_gencode_v19_CTAT_lib_Oct012019/ctat_genome_lib_build_dir/' --output_folder 's3://fh-pi-meshinchi-s-eco-public/TARGET_AML/RNAseq_Illumina_Data/STAR_Fusion/' --multiQC 's3://fh-pi-meshinchi-s-eco-public/TARGET_AML/RNAseq_Illumina_Data/multiQC/' --cicero_genome_lib 's3://fh-pi-meshinchi-s-eco-public/Reference_Data/CICERO_Ref/' --CICERO 's3://fh-pi-meshinchi-s-eco-public/TARGET_AML/RNAseq_Illumina_Data/CICERO/' -with-report STAR-Fusion_Remission_JMML_APL_MDAnderson_AML_report.html -cache TRUE -resume
CPU-Hours
1'970.1 (7.9% cached, 27% failed)
Launch directory
/home/jlsmith3/scripts/STAR-fusion-NF
Work directory
s3://fh-pi-meshinchi-s-nextflow-scratch/
Project directory
/home/jlsmith3/scripts/STAR-fusion-NF
Script name
main.nf
Script ID
80a6aeca4093f275d7bf3365e2f9bc57
Workflow session
9d18987c-7583-4533-95dc-4969dd673b38
Workflow profile
standard
Nextflow version
version 20.07.1, build 5412 (24-07-2020 15:18 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)